Zuelania guidonia is a tree species of cultural importance in Totonac society. This tree is a central element of the Los Voladores (the "flying men") pre-Hispanic ritual ceremony. However, the populations of Z. guidonia have decreased due to anthropogenic activity. This study aimed to codesign an agroforestry model for the recovery of Z. guidonia populations by combining scientific and traditional agroforestry knowledge at the El Tajín archaeological site in Veracruz, Mexico. We assessed the abundance of Z. guidonia and analyzed plant species richness and diversity in forest fragments. Species were classified according to plant regeneration modes (light-demanding and shade-tolerant) and to the local uses of secondary forests and conserved forest fragments. In addition, we worked collaboratively in a project that consisted of workshops, focus groups, open interviews, drawings, and field walks with community members. We studied a small population of Z. guidonia and recorded 116 woody species. Our findings showed that conserved forests were more diverse than secondary forests. Seventy-four percent of the species are useful to people. The Totonac people chose traditional vanilla plantations as a guiding model to shape their agroforestry system for restoring native vegetation. The results of our collaborative work revealed the Totonac extensive Traditional Ecological Knowledge and the need for the Voladores' group to strengthen alliances with other government and nongovernment organizations. They designed a model of a diversified traditional agroforestry vanilla system enriched with multipurpose plants as the outset of local well-being and regional agrobiodiversity restoration. This study reveals a distinct heterogenous land management scheme that provides the necessary conditions for preserving plant diversity, which will be used by local people for different purposes. We argue for studies that build on the relationship between scientific knowledge and Traditional Ecological Knowledge in transformed landscapes as a step forward for the long-term conservation of biocultural diversity.